This is a topic that comes up at every stage of the brand development process. It is a great topic and has been asked at a couple of sessions that I was facilitating over the past week. In the beginning people have a tendency to think when an organization decides to move forward with a brand initiative, that the organization is deciding to dilute or eliminate their sub-brands. While this might be the case in certain situations, I certainly do not adhere to that kind of strategy.
It is important to be aware that many of your stakeholders have this concern. So, whatever the motives for moving forward with a brand plan, you need to inform your people what your intentions are at every stage of the process. I advocate that you tell your stakeholders how much you value the work that they have put into developing a sub-brand (i.e.- department, institute, partnership) and that your decision is to create an overarching brand strategy, while at the same time providing every opportunity to maintain the essence of the sub-brands.
No matter what direction you take with your brand strategy development, you will be able to recruit and retain your brand champions by being informative and helping them understand the relevancy of your decisions.